I think you're right. The master level problem uses (row/column)-order as was said in their forum. Other than that, the example for the apprentice level problem is the first problem ofhttp://www.clickmazes.com/life/ixlife.htmwhich shows that the apprentice level problem uses (row/column)-order, too.

I concur that the coordinate order is (row column) - also known as (y x).

Two things unambiguosly stated are that (1 1) is the upper left corner and direction '1' moves to the upper left. Given those facts, the solution to the sample problem 3845524 moves four cells to the right. If the coordinates had been in (x y) order then the solution would have to move in a downward direction.

Like malumalu said, the first problem at clickmazes helps to visualize the example.